DGE analysis of mPFC

MA plots

Removing L0001

## geom_smooth: se = FALSE, na.rm = FALSE, orientation = NA
## stat_smooth: method = loess, formula = y ~ x, se = FALSE, n = 80, fullrange = FALSE, level = 0.95, na.rm = FALSE, orientation = NA, method.args = list(), span = 0.75
## position_identity
## Warning: Use of `res$AveExpr` is discouraged. Use `AveExpr` instead.
## Warning: Use of `res$logFC` is discouraged. Use `logFC` instead.
## Warning: Use of `res_l1$AveExpr` is discouraged. Use `AveExpr` instead.
## Warning: Use of `res_l1$logFC` is discouraged. Use `logFC` instead.

PCA

All samples

pca <- prcomp(t(data$cpm))
# ggplotly(
  pc1 <- autoplot(pca,
  data = data$pData, colour = "Group",
  frame = TRUE, frame.type = "norm", size = 5
) +
  ggtitle("") + 
    theme_bw() +
    scale_color_manual(values=brewer.pal(n = 3, name = "Set1")[1:2]) +
    theme(axis.text.x = element_text(size = 20, colour = "black"),
        axis.text.y = element_text(size = 20, colour = "black"),  
        axis.title.x = element_text(size = 20, colour = "black"),
        axis.title.y = element_text(size = 20, colour = "black"),
        plot.title = element_text(size = 25, face = "bold", colour = "black"),
        legend.text=element_text(size=20, colour = "black"),
        legend.title=element_text(size=20, face = "bold"),
        panel.border = element_rect(colour = "black", fill=NA, size=2))
    
  
  pc2 <- autoplot(pca,
  data = data$pData, colour = "Lane",
  frame = TRUE, frame.type = "norm", size = 5
) +
  ggtitle("") + 
    theme_bw()+
    scale_color_manual(values=brewer.pal(n = 3, name = "Set1")[1:2]) +
    theme(axis.text.x = element_text(size = 20),
        axis.text.y = element_text(size = 20),  
        axis.title.x = element_text(size = 20),
        axis.title.y = element_text(size = 20),
        plot.title = element_text(size = 25, face = "bold"),
        legend.text=element_text(size=20),
        legend.title=element_text(size=20, face = "bold"),
        panel.border = element_rect(colour = "black", fill=NA, size=2))
  
  
  pca1 <- prcomp(t(data$cpm[,-1]))
# ggplotly(
  pc3 <- autoplot(pca1,
  data = data$pData[-1,], colour = "Group",
  frame = TRUE, frame.type = "norm", size = 5
) +
  ggtitle("") + 
    theme_bw() +
    scale_color_manual(values=brewer.pal(n = 3, name = "Set1")[1:2]) +
    theme(axis.text.x = element_text(size = 20, colour = "black"),
        axis.text.y = element_text(size = 20, colour = "black"),  
        axis.title.x = element_text(size = 20, colour = "black"),
        axis.title.y = element_text(size = 20, colour = "black"),
        plot.title = element_text(size = 25, face = "bold", colour = "black"),
        legend.text=element_text(size=20, colour = "black"),
        legend.title=element_text(size=20, face = "bold"),
        panel.border = element_rect(colour = "black", fill=NA, size=2))
## Too few points to calculate an ellipse
## Too few points to calculate an ellipse
## Too few points to calculate an ellipse

## Too few points to calculate an ellipse
## Too few points to calculate an ellipse

All samples

## 
## Attaching package: 'plotly'
## The following object is masked from 'package:IRanges':
## 
##     slice
## The following object is masked from 'package:S4Vectors':
## 
##     rename
## The following object is masked from 'package:ggplot2':
## 
##     last_plot
## The following object is masked from 'package:stats':
## 
##     filter
## The following object is masked from 'package:graphics':
## 
##     layout
## Warning: `arrange_()` is deprecated as of dplyr 0.7.0.
## Please use `arrange()` instead.
## See vignette('programming') for more help
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_warnings()` to see where this warning was generated.
## Warning in RColorBrewer::brewer.pal(N, "Set2"): minimal value for n is 3, returning requested palette with 3 different levels

## Warning in RColorBrewer::brewer.pal(N, "Set2"): minimal value for n is 3, returning requested palette with 3 different levels
## Warning: Didn't find a colorbar to modify.

Remove L1

## Warning in RColorBrewer::brewer.pal(N, "Set2"): minimal value for n is 3, returning requested palette with 3 different levels

## Warning in RColorBrewer::brewer.pal(N, "Set2"): minimal value for n is 3, returning requested palette with 3 different levels
## Warning: Didn't find a colorbar to modify.

Fig

References

## Warning in citation(pkg_name): no date field in DESCRIPTION file of package
## 'plgINS'

SessionInfo


─ Session info ───────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 3.6.2 (2019-12-12)
 os       Ubuntu 16.04.7 LTS          
 system   x86_64, linux-gnu           
 ui       X11                         
 language (EN)                        
 collate  de_DE.UTF-8                 
 ctype    de_DE.UTF-8                 
 tz       Europe/Zurich               
 date     2020-11-10                  

─ Packages ───────────────────────────────────────────────────────────────────
 package              * version    date       lib
 annotate               1.64.0     2019-10-29 [1]
 AnnotationDbi          1.48.0     2019-10-29 [1]
 assertthat             0.2.1      2019-03-21 [1]
 autoplotly           * 0.1.2      2018-04-21 [1]
 backports              1.1.8      2020-06-17 [1]
 base64enc              0.1-3      2015-07-28 [1]
 Biobase              * 2.46.0     2019-10-29 [1]
 BiocGenerics         * 0.32.0     2019-10-29 [1]
 BiocManager            1.30.10    2019-11-16 [1]
 BiocParallel         * 1.20.1     2019-12-21 [1]
 Biostrings             2.54.0     2019-10-29 [1]
 bit                    4.0.4      2020-08-04 [1]
 bit64                  4.0.2      2020-07-30 [1]
 bitops                 1.0-6      2013-08-17 [1]
 blob                   1.2.1      2020-01-20 [1]
 bookdown               0.20       2020-06-23 [1]
 callr                  3.4.3      2020-03-28 [1]
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 data.table             1.13.0     2020-07-24 [1]
 DBI                    1.1.0      2019-12-15 [1]
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 desc                   1.2.0      2018-05-01 [1]
 DESeq2                 1.26.0     2019-10-29 [1]
 devtools               2.3.1      2020-07-21 [1]
 digest                 0.6.25     2020-02-23 [1]
 dplyr                * 1.0.1      2020-07-31 [1]
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 evaluate               0.14       2019-05-28 [1]
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 Formula                1.2-3      2018-05-03 [1]
 fs                     1.5.0      2020-07-31 [1]
 genefilter           * 1.68.0     2019-10-29 [1]
 geneplotter            1.64.0     2019-10-29 [1]
 generics               0.0.2      2018-11-29 [1]
 GenomeInfoDb         * 1.22.1     2020-03-27 [1]
 GenomeInfoDbData       1.2.2      2019-11-18 [1]
 GenomicRanges        * 1.38.0     2019-10-29 [1]
 GEOquery               2.54.1     2019-11-18 [1]
 ggfortify              0.4.10     2020-07-27 [1]
 ggplot2              * 3.3.2      2020-06-19 [1]
 ggplotify            * 0.0.5      2020-03-12 [1]
 glue                   1.4.1      2020-05-13 [1]
 gridExtra              2.3        2017-09-09 [1]
 gridGraphics           0.5-0      2020-02-25 [1]
 gtable                 0.3.0      2019-03-25 [1]
 Hmisc                  4.4-1      2020-08-10 [1]
 hms                    0.5.3      2020-01-08 [1]
 htmlTable              2.0.1      2020-07-05 [1]
 htmltools              0.5.0      2020-06-16 [1]
 htmlwidgets            1.5.1      2019-10-08 [1]
 httr                   1.4.2      2020-07-20 [1]
 insight                0.9.0      2020-07-20 [1]
 IRanges              * 2.20.2     2020-01-13 [1]
 jpeg                   0.1-8.1    2019-10-24 [1]
 jsonlite               1.7.0      2020-06-25 [1]
 knitr                  1.29       2020-06-23 [1]
 labeling               0.3        2014-08-23 [1]
 lattice                0.20-41    2020-04-02 [1]
 latticeExtra           0.6-29     2019-12-19 [1]
 lazyeval               0.2.2      2019-03-15 [1]
 lifecycle              0.2.0      2020-03-06 [1]
 limma                * 3.42.2     2020-02-03 [1]
 locfit                 1.5-9.4    2020-03-25 [1]
 magrittr               1.5        2014-11-22 [1]
 Matrix                 1.2-18     2019-11-27 [1]
 matrixStats          * 0.56.0     2020-03-13 [1]
 memoise                1.1.0.9000 2020-05-06 [1]
 mgcv                 * 1.8-31     2019-11-09 [1]
 munsell                0.5.0      2018-06-12 [1]
 nlme                 * 3.1-148    2020-05-24 [1]
 nnet                   7.3-14     2020-04-26 [1]
 patchwork            * 1.0.1      2020-06-22 [1]
 pheatmap             * 1.0.12     2019-01-04 [1]
 pillar                 1.4.6      2020-07-10 [1]
 pkgbuild               1.1.0      2020-07-13 [1]
 pkgconfig              2.0.3      2019-09-22 [1]
 pkgload                1.1.0      2020-05-29 [1]
 plgINS               * 0.1.5      2020-07-10 [1]
 plotly               * 4.9.2.1    2020-04-04 [1]
 plyr                   1.8.6      2020-03-03 [1]
 png                    0.1-7      2013-12-03 [1]
 prettyunits            1.1.1      2020-01-24 [1]
 processx               3.4.3      2020-07-05 [1]
 ps                     1.3.3      2020-05-08 [1]
 purrr                  0.3.4      2020-04-17 [1]
 R6                     2.4.1      2019-11-12 [1]
 RColorBrewer         * 1.1-2      2014-12-07 [1]
 Rcpp                   1.0.5      2020-07-06 [1]
 RCurl                  1.98-1.2   2020-04-18 [1]
 readr                  1.3.1      2018-12-21 [1]
 remotes                2.2.0      2020-07-21 [1]
 report                 0.1.0      2020-03-19 [1]
 reshape2             * 1.4.4      2020-04-09 [1]
 rlang                  0.4.7      2020-07-09 [1]
 rmarkdown              2.3        2020-06-18 [1]
 rmdformats             0.4.0      2020-06-07 [1]
 rpart                  4.1-15     2019-04-12 [1]
 rprojroot              1.3-2      2018-01-03 [1]
 RSQLite                2.1.4      2019-12-04 [1]
 rstudioapi             0.11       2020-02-07 [1]
 rvcheck                0.1.8      2020-03-01 [1]
 S4Vectors            * 0.24.4     2020-04-09 [1]
 scales                 1.1.1      2020-05-11 [1]
 sessioninfo            1.1.1      2018-11-05 [1]
 SRAdb                  1.48.2     2019-12-24 [1]
 stringi                1.4.6      2020-02-17 [1]
 stringr                1.4.0      2019-02-10 [1]
 SummarizedExperiment * 1.16.1     2019-12-19 [1]
 survival               3.2-3      2020-06-13 [1]
 sva                  * 3.34.0     2019-10-29 [1]
 testthat               2.3.2      2020-03-02 [1]
 tibble                 3.0.3      2020-07-10 [1]
 tidyr                  1.1.0      2020-05-20 [1]
 tidyselect             1.1.0      2020-05-11 [1]
 usethis                1.6.1      2020-04-29 [1]
 vctrs                  0.3.2      2020-07-15 [1]
 viridis              * 0.5.1      2018-03-29 [1]
 viridisLite          * 0.3.0      2018-02-01 [1]
 withr                  2.2.0      2020-04-20 [1]
 writexl                1.3        2020-05-05 [1]
 xfun                   0.16       2020-07-24 [1]
 XML                    3.99-0.3   2020-01-20 [1]
 xml2                   1.3.2      2020-04-23 [1]
 xtable                 1.8-4      2019-04-21 [1]
 XVector                0.26.0     2019-10-29 [1]
 yaml                   2.2.1      2020-02-01 [1]
 zlibbioc               1.32.0     2019-10-29 [1]
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[1] /home/ubuntu/R/x86_64-pc-linux-gnu-library/3.6
[2] /usr/local/lib/R/site-library
[3] /usr/lib/R/site-library
[4] /usr/lib/R/library